One of the great new features in iTunes 9 is app management; I've been begging for this one (among other things). We can now organize our pages (and pages) of apps right in iTunes, no more dragging jiggly icons across 9 or 10 screens. I'm ecstatic (and wondering what took so long).
From Apple's website:
[...] it's easier to organize all the apps on your iPhone or iPod touch, because now you can do it right in iTunes, right from your computer. Shop the App Store on your computer, iPhone, or iPod touch. Then go to your iTunes library to arrange (and rearrange) your apps and add (or delete) Home screens. iTunes automatically syncs your new Home screens with your iPhone or iPod touch.